Starting phenix.real_space_refine
on Tue Aug  4 14:12:22 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/26ve_80907/08_2026/26ve_80907.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/26ve_80907/08_2026/26ve_80907.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/26ve_80907/08_2026/26ve_80907.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/26ve_80907/08_2026/26ve_80907.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/26ve_80907/08_2026/26ve_80907.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/26ve_80907/08_2026/26ve_80907.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    2482      2.51       5
     N     580      2.21       5
     O     627      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3718
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 484, 3718
          Classifications: {'peptide': 484}
          Link IDs: {'PTRANS': 22, 'TRANS': 461}
          Chain breaks: 2
  Time building chain proxies: 0.67, per 1000 atoms: 0.18
  Number of scatterers: 3718
  At special positions: 0
  Unit cell: (78.02, 68.06, 75.53, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O     627      8.00
     N     580      7.00
     C    2482      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 88.7 milliseconds
  

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  878

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      82.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 47
    Processing helix  chain 'A' and resid 71 through 79
    Processing helix  chain 'A' and resid 82 through 87
    Processing helix  chain 'A' and resid 87 through 96
    Processing helix  chain 'A' and resid 98 through 104
    Processing helix  chain 'A' and resid 105 through 110
    Processing helix  chain 'A' and resid 110 through 116
    Processing helix  chain 'A' and resid 116 through 123
    Processing helix  chain 'A' and resid 130 through 137
      removed outlier: 3.700A  pdb=" N   GLU A 134 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 173
      Proline residue:  A 164  - end of helix
    Processing helix  chain 'A' and resid 175 through 193
    Processing helix  chain 'A' and resid 202 through 226
    Processing helix  chain 'A' and resid 227 through 238
    Processing helix  chain 'A' and resid 255 through 272
    Processing helix  chain 'A' and resid 274 through 283
      removed outlier: 4.010A  pdb=" N   ARG A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 322
      removed outlier: 3.656A  pdb=" N   ALA A 290 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   PHE A 298 " --> pdb=" O   CYS A 294 " (cutoff:3.500A)
      Proline residue:  A 299  - end of helix
    Processing helix  chain 'A' and resid 325 through 330
      removed outlier: 3.682A  pdb=" N   ALA A 329 " --> pdb=" O   SER A 325 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLN A 330 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 325 through 330'
    Processing helix  chain 'A' and resid 335 through 345
    Processing helix  chain 'A' and resid 350 through 383
      removed outlier: 3.778A  pdb=" N   ILE A 383 " --> pdb=" O   MET A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 417
      removed outlier: 3.523A  pdb=" N   ILE A 396 " --> pdb=" O   GLU A 392 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   MET A 397 " --> pdb=" O   ALA A 393 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   GLY A 401 " --> pdb=" O   MET A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 434
    Processing helix  chain 'A' and resid 434 through 448
      removed outlier: 3.686A  pdb=" N   LEU A 438 " --> pdb=" O   VAL A 434 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   PHE A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 476
    Processing helix  chain 'A' and resid 529 through 549
      removed outlier: 3.858A  pdb=" N   LEU A 543 " --> pdb=" O   ILE A 539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 569

    279 hydrogen bonds defined for protein.
    825 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.56

  Time building geometry restraints manager: 0.43 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 1064
        1.34 -     1.46: 727
        1.46 -     1.57: 1981
        1.57 -     1.69: 0
        1.69 -     1.81: 47
  Bond restraints: 3819
  Sorted by residual:
  bond pdb=" CB  VAL A 538 "
       pdb=" CG2 VAL A 538 "
    ideal  model  delta    sigma   weight residual
    1.521  1.456  0.065 3.30e-02 9.18e+02 3.84e+00
  bond pdb=" C   PRO A 453 "
       pdb=" N   PRO A 454 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.23e-02 6.61e+03 2.43e+00
  bond pdb=" CB  MET A 315 "
       pdb=" CG  MET A 315 "
    ideal  model  delta    sigma   weight residual
    1.520  1.479  0.041 3.00e-02 1.11e+03 1.84e+00
  bond pdb=" CG  LEU A 338 "
       pdb=" CD1 LEU A 338 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.83e+00
  bond pdb=" C   PHE A 298 "
       pdb=" N   PRO A 299 "
    ideal  model  delta    sigma   weight residual
    1.336  1.352 -0.016 1.20e-02 6.94e+03 1.77e+00
  ... (remaining 3814 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 4930
        1.81 -     3.61: 228
        3.61 -     5.42: 30
        5.42 -     7.22: 10
        7.22 -     9.03: 6
  Bond angle restraints: 5204
  Sorted by residual:
  angle pdb=" N   PRO A 453 "
        pdb=" CA  PRO A 453 "
        pdb=" C   PRO A 453 "
      ideal   model   delta    sigma   weight residual
     110.70  115.65   -4.95 1.22e+00 6.72e-01 1.65e+01
  angle pdb=" N   LEU A 351 "
        pdb=" CA  LEU A 351 "
        pdb=" C   LEU A 351 "
      ideal   model   delta    sigma   weight residual
     109.81  118.19   -8.38 2.21e+00 2.05e-01 1.44e+01
  angle pdb=" CA  PRO A 453 "
        pdb=" C   PRO A 453 "
        pdb=" N   PRO A 454 "
      ideal   model   delta    sigma   weight residual
     117.93  122.29   -4.36 1.20e+00 6.94e-01 1.32e+01
  angle pdb=" CG1 ILE A 367 "
        pdb=" CB  ILE A 367 "
        pdb=" CG2 ILE A 367 "
      ideal   model   delta    sigma   weight residual
     110.70  101.77    8.93 3.00e+00 1.11e-01 8.86e+00
  angle pdb=" C   GLY A 350 "
        pdb=" N   LEU A 351 "
        pdb=" CA  LEU A 351 "
      ideal   model   delta    sigma   weight residual
     121.80  128.76   -6.96 2.44e+00 1.68e-01 8.14e+00
  ... (remaining 5199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.42: 2093
       15.42 -    30.85: 65
       30.85 -    46.27: 17
       46.27 -    61.69: 2
       61.69 -    77.11: 4
  Dihedral angle restraints: 2181
    sinusoidal: 798
      harmonic: 1383
  Sorted by residual:
  dihedral pdb=" CA  HIS A 254 "
           pdb=" C   HIS A 254 "
           pdb=" N   THR A 255 "
           pdb=" CA  THR A 255 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.75   23.25     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  SER A  25 "
           pdb=" C   SER A  25 "
           pdb=" N   ILE A  26 "
           pdb=" CA  ILE A  26 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.69   18.31     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  MET A 157 "
           pdb=" C   MET A 157 "
           pdb=" N   GLY A 158 "
           pdb=" CA  GLY A 158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.48   17.52     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 2178 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 397
       0.043 -    0.087: 156
       0.087 -    0.130: 50
       0.130 -    0.173: 7
       0.173 -    0.216: 1
  Chirality restraints: 611
  Sorted by residual:
  chirality pdb=" CB  VAL A 231 "
            pdb=" CA  VAL A 231 "
            pdb=" CG1 VAL A 231 "
            pdb=" CG2 VAL A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  LEU A 351 "
            pdb=" N   LEU A 351 "
            pdb=" C   LEU A 351 "
            pdb=" CB  LEU A 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.16e-01
  chirality pdb=" CB  ILE A 367 "
            pdb=" CA  ILE A 367 "
            pdb=" CG1 ILE A 367 "
            pdb=" CG2 ILE A 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.16 2.00e-01 2.50e+01 6.13e-01
  ... (remaining 608 not shown)

  Planarity restraints: 633
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 371 "   -0.016 2.00e-02 2.50e+03   1.80e-02 5.65e+00
        pdb=" CG  PHE A 371 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 371 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 371 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 371 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 371 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 371 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 436 "    0.036 5.00e-02 4.00e+02   5.49e-02 4.81e+00
        pdb=" N   PRO A 437 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 437 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 437 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 452 "    0.034 5.00e-02 4.00e+02   5.11e-02 4.19e+00
        pdb=" N   PRO A 453 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 453 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 453 "    0.028 5.00e-02 4.00e+02
  ... (remaining 630 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1070
        2.81 -     3.33: 3492
        3.33 -     3.86: 6160
        3.86 -     4.38: 6978
        4.38 -     4.90: 12111
  Nonbonded interactions: 29811
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 473 "
            pdb=" OG1 THR A 477 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   GLY A 542 "
            pdb=" OG  SER A 546 "
     model   vdw
     2.362 3.040
  nonbonded pdb=" O   LEU A 374 "
            pdb=" OG1 THR A 378 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" O   SER A 222 "
            pdb=" N   GLY A 227 "
     model   vdw
     2.394 3.120
  nonbonded pdb=" O   GLY A 432 "
            pdb=" ND2 ASN A 534 "
     model   vdw
     2.396 3.120
  ... (remaining 29806 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.100
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   3819  Z= 0.238
  Angle     :  0.921   9.028   5204  Z= 0.499
  Chirality :  0.050   0.216    611
  Planarity :  0.008   0.055    633
  Dihedral  :  9.853  77.114   1303
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.63 (0.29), residues: 478
  helix: -2.15 (0.20), residues: 379
  sheet:  None (None), residues: 0
  loop : -2.50 (0.51), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 280 
 TYR   0.023   0.002   TYR A 281 
 PHE   0.040   0.003   PHE A 371 
 TRP   0.026   0.002   TRP A 469 
 HIS   0.011   0.002   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00543 /  0.24 ( 3819)
  covalent geometry    : angle       0.92141 /  0.50 ( 5204)
  hydrogen bonds       : bond        0.12678 /  7.88 (  279)
  hydrogen bonds       : angle       6.92267 /  4.52 (  825)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LEU cc_start: 0.7885 (mm) cc_final: 0.7568 (tp)
REVERT: A   97 THR cc_start: 0.8725 (p) cc_final: 0.8185 (t)
REVERT: A  135 LEU cc_start: 0.7420 (tp) cc_final: 0.7030 (mp)
REVERT: A  153 MET cc_start: 0.7531 (mmm) cc_final: 0.6543 (tpp)
REVERT: A  253 ARG cc_start: 0.7768 (ttt-90) cc_final: 0.7427 (ttt-90)
REVERT: A  318 TYR cc_start: 0.8573 (t80) cc_final: 0.8211 (t80)
REVERT: A  361 SER cc_start: 0.8720 (m) cc_final: 0.8422 (t)
REVERT: A  431 PHE cc_start: 0.8199 (m-80) cc_final: 0.7968 (m-10)
REVERT: A  460 LEU cc_start: 0.8503 (tp) cc_final: 0.7929 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0652
  time to fit residues: 11.8946
Evaluate side-chains
  103 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.3980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 419 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.167530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.139735 restraints weight = 4698.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.144428 restraints weight = 2488.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.147873 restraints weight = 1602.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.150222 restraints weight = 1167.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.151508 restraints weight = 935.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3819  Z= 0.152
  Angle     :  0.628   7.283   5204  Z= 0.322
  Chirality :  0.040   0.137    611
  Planarity :  0.006   0.044    633
  Dihedral  :  4.528  19.841    520
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.10 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.37), residues: 478
  helix: -0.11 (0.26), residues: 378
  sheet:  None (None), residues: 0
  loop : -1.55 (0.60), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 142 
 TYR   0.020   0.002   TYR A  99 
 PHE   0.038   0.002   PHE A 137 
 TRP   0.022   0.002   TRP A 469 
 HIS   0.005   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.15 ( 3819)
  covalent geometry    : angle       0.62781 /  0.32 ( 5204)
  hydrogen bonds       : bond        0.03809 /  2.53 (  279)
  hydrogen bonds       : angle       4.73759 /  3.10 (  825)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A   36 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7493 (tp)
REVERT: A   97 THR cc_start: 0.8560 (p) cc_final: 0.8060 (t)
REVERT: A   98 GLN cc_start: 0.8426 (tp40) cc_final: 0.8153 (tp40)
REVERT: A  130 TYR cc_start: 0.8187 (m-80) cc_final: 0.7799 (m-10)
REVERT: A  135 LEU cc_start: 0.7199 (tp) cc_final: 0.6796 (mp)
REVERT: A  157 MET cc_start: 0.7181 (mmt) cc_final: 0.6347 (mmt)
REVERT: A  174 PHE cc_start: 0.5934 (t80) cc_final: 0.5521 (t80)
REVERT: A  275 GLN cc_start: 0.7617 (tp40) cc_final: 0.7274 (tp40)
REVERT: A  320 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7569 (mm-40)
REVERT: A  360 PHE cc_start: 0.7776 (t80) cc_final: 0.7559 (t80)
REVERT: A  361 SER cc_start: 0.8833 (m) cc_final: 0.8598 (t)
REVERT: A  379 MET cc_start: 0.8368 (mmp) cc_final: 0.7959 (mmp)
REVERT: A  425 GLN cc_start: 0.8061 (tt0) cc_final: 0.7541 (tp40)
  outliers start: 11
  outliers final: 5
  residues processed: 116
  average time/residue: 0.0434
  time to fit residues: 6.9776
Evaluate side-chains
  104 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  320 GLN
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  531 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 45 optimal weight:    0.1980
   chunk 38 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0270
   chunk 37 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.4238

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 328 GLN
A 419 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.167281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.141004 restraints weight = 4644.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.145434 restraints weight = 2558.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.148564 restraints weight = 1676.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.150516 restraints weight = 1232.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.152078 restraints weight = 997.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3819  Z= 0.127
  Angle     :  0.584   6.729   5204  Z= 0.298
  Chirality :  0.039   0.144    611
  Planarity :  0.005   0.047    633
  Dihedral  :  4.218  15.908    520
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 13.35 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.39), residues: 478
  helix:  0.71 (0.27), residues: 378
  sheet:  None (None), residues: 0
  loop : -1.37 (0.62), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 142 
 TYR   0.014   0.001   TYR A  99 
 PHE   0.025   0.002   PHE A 137 
 TRP   0.019   0.002   TRP A 469 
 HIS   0.004   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 3819)
  covalent geometry    : angle       0.58393 /  0.30 ( 5204)
  hydrogen bonds       : bond        0.03523 /  2.34 (  279)
  hydrogen bonds       : angle       4.42318 /  2.92 (  825)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7503 (tp)
REVERT: A   97 THR cc_start: 0.8569 (p) cc_final: 0.8073 (t)
REVERT: A  135 LEU cc_start: 0.7148 (tp) cc_final: 0.6718 (mp)
REVERT: A  157 MET cc_start: 0.7223 (mmt) cc_final: 0.6622 (mmt)
REVERT: A  281 TYR cc_start: 0.7858 (m-80) cc_final: 0.7531 (m-10)
REVERT: A  318 TYR cc_start: 0.8451 (t80) cc_final: 0.8141 (t80)
REVERT: A  320 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7655 (mm-40)
REVERT: A  342 MET cc_start: 0.8223 (mmm) cc_final: 0.7878 (mmt)
REVERT: A  361 SER cc_start: 0.8838 (m) cc_final: 0.8575 (t)
REVERT: A  384 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7874 (ttm-80)
  outliers start: 13
  outliers final: 4
  residues processed: 109
  average time/residue: 0.0358
  time to fit residues: 5.3834
Evaluate side-chains
  100 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  320 GLN
Chi-restraints excluded: chain A residue  328 GLN
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  531 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 12 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 47 optimal weight:    0.4980
   chunk 17 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 419 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.162963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.136007 restraints weight = 4734.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.140617 restraints weight = 2531.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.143889 restraints weight = 1618.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.145892 restraints weight = 1177.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.147416 restraints weight = 950.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.3252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3819  Z= 0.158
  Angle     :  0.630   7.608   5204  Z= 0.314
  Chirality :  0.041   0.142    611
  Planarity :  0.004   0.049    633
  Dihedral  :  4.138  16.310    520
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 15.37 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.40), residues: 478
  helix:  0.97 (0.28), residues: 380
  sheet:  None (None), residues: 0
  loop : -1.25 (0.63), residues: 98

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 136 
 TYR   0.021   0.001   TYR A  99 
 PHE   0.022   0.002   PHE A 431 
 TRP   0.020   0.001   TRP A 469 
 HIS   0.006   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.16 ( 3819)
  covalent geometry    : angle       0.62952 /  0.31 ( 5204)
  hydrogen bonds       : bond        0.03605 /  2.39 (  279)
  hydrogen bonds       : angle       4.35602 /  2.88 (  825)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A   36 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7583 (tp)
REVERT: A   97 THR cc_start: 0.8652 (p) cc_final: 0.8120 (t)
REVERT: A  100 TRP cc_start: 0.6197 (t60) cc_final: 0.5963 (t60)
REVERT: A  130 TYR cc_start: 0.8313 (m-80) cc_final: 0.8099 (m-10)
REVERT: A  135 LEU cc_start: 0.7281 (tp) cc_final: 0.6765 (mp)
REVERT: A  153 MET cc_start: 0.7943 (tpt) cc_final: 0.7296 (tpp)
REVERT: A  157 MET cc_start: 0.7437 (mmt) cc_final: 0.6687 (mmt)
REVERT: A  275 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7778 (tm-30)
REVERT: A  281 TYR cc_start: 0.7887 (m-80) cc_final: 0.7658 (m-10)
REVERT: A  361 SER cc_start: 0.8904 (m) cc_final: 0.8582 (t)
  outliers start: 10
  outliers final: 5
  residues processed: 100
  average time/residue: 0.0281
  time to fit residues: 3.8809
Evaluate side-chains
  92 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  531 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0040
   chunk 24 optimal weight:    0.8980
   chunk 35 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6592

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.187034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.159002 restraints weight = 4439.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.163805 restraints weight = 2475.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.167143 restraints weight = 1620.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.169324 restraints weight = 1197.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.171100 restraints weight = 966.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3819  Z= 0.141
  Angle     :  0.597   6.990   5204  Z= 0.300
  Chirality :  0.040   0.146    611
  Planarity :  0.004   0.051    633
  Dihedral  :  4.140  17.582    520
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.64 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.40), residues: 478
  helix:  1.18 (0.28), residues: 378
  sheet:  None (None), residues: 0
  loop : -1.13 (0.64), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 384 
 TYR   0.016   0.001   TYR A  99 
 PHE   0.019   0.002   PHE A 137 
 TRP   0.021   0.001   TRP A 469 
 HIS   0.005   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.14 ( 3819)
  covalent geometry    : angle       0.59677 /  0.30 ( 5204)
  hydrogen bonds       : bond        0.03498 /  2.32 (  279)
  hydrogen bonds       : angle       4.27474 /  2.83 (  825)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A   36 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7564 (tp)
REVERT: A   97 THR cc_start: 0.8674 (p) cc_final: 0.8136 (t)
REVERT: A  100 TRP cc_start: 0.6167 (t60) cc_final: 0.5943 (t60)
REVERT: A  135 LEU cc_start: 0.7336 (tp) cc_final: 0.6799 (mp)
REVERT: A  157 MET cc_start: 0.7506 (mmt) cc_final: 0.6773 (mmt)
REVERT: A  275 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7806 (tm-30)
REVERT: A  361 SER cc_start: 0.8897 (m) cc_final: 0.8566 (t)
REVERT: A  379 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7759 (mmp)
  outliers start: 8
  outliers final: 4
  residues processed: 90
  average time/residue: 0.0447
  time to fit residues: 5.5779
Evaluate side-chains
  92 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  528 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.160675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.134153 restraints weight = 4725.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.138418 restraints weight = 2599.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.141579 restraints weight = 1705.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.143566 restraints weight = 1256.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.145272 restraints weight = 1015.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3819  Z= 0.154
  Angle     :  0.615   7.286   5204  Z= 0.311
  Chirality :  0.040   0.148    611
  Planarity :  0.004   0.052    633
  Dihedral  :  4.121  17.627    520
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.40 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.40), residues: 478
  helix:  1.26 (0.28), residues: 377
  sheet:  None (None), residues: 0
  loop : -1.03 (0.64), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 136 
 TYR   0.012   0.001   TYR A  99 
 PHE   0.018   0.002   PHE A 316 
 TRP   0.022   0.001   TRP A 469 
 HIS   0.005   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.15 ( 3819)
  covalent geometry    : angle       0.61454 /  0.31 ( 5204)
  hydrogen bonds       : bond        0.03555 /  2.33 (  279)
  hydrogen bonds       : angle       4.30514 /  2.86 (  825)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A   36 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7579 (tp)
REVERT: A   97 THR cc_start: 0.8720 (p) cc_final: 0.8129 (t)
REVERT: A  100 TRP cc_start: 0.6114 (t60) cc_final: 0.5897 (t60)
REVERT: A  135 LEU cc_start: 0.7455 (tp) cc_final: 0.6787 (mp)
REVERT: A  157 MET cc_start: 0.7625 (mmt) cc_final: 0.6833 (mmt)
REVERT: A  275 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7767 (tm-30)
REVERT: A  361 SER cc_start: 0.8929 (m) cc_final: 0.8581 (t)
REVERT: A  382 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7523 (mt)
  outliers start: 9
  outliers final: 6
  residues processed: 98
  average time/residue: 0.0296
  time to fit residues: 4.0330
Evaluate side-chains
  96 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  382 LEU
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  531 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.161985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.134337 restraints weight = 4777.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.138999 restraints weight = 2592.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.142444 restraints weight = 1680.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.144536 restraints weight = 1225.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.146258 restraints weight = 986.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   3819  Z= 0.152
  Angle     :  0.632   8.227   5204  Z= 0.315
  Chirality :  0.041   0.156    611
  Planarity :  0.004   0.053    633
  Dihedral  :  4.138  17.753    520
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 19.65 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.41), residues: 478
  helix:  1.34 (0.28), residues: 377
  sheet:  None (None), residues: 0
  loop : -1.03 (0.65), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 384 
 TYR   0.011   0.001   TYR A  99 
 PHE   0.016   0.001   PHE A 137 
 TRP   0.022   0.001   TRP A 469 
 HIS   0.004   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.15 ( 3819)
  covalent geometry    : angle       0.63219 /  0.31 ( 5204)
  hydrogen bonds       : bond        0.03452 /  2.27 (  279)
  hydrogen bonds       : angle       4.27073 /  2.84 (  825)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   36 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7605 (tp)
REVERT: A   97 THR cc_start: 0.8736 (p) cc_final: 0.8168 (t)
REVERT: A  100 TRP cc_start: 0.5991 (t60) cc_final: 0.5334 (t60)
REVERT: A  174 PHE cc_start: 0.5421 (OUTLIER) cc_final: 0.5191 (t80)
REVERT: A  275 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7982 (tm-30)
REVERT: A  342 MET cc_start: 0.8761 (mmm) cc_final: 0.8440 (mmt)
REVERT: A  361 SER cc_start: 0.8945 (m) cc_final: 0.8632 (t)
  outliers start: 8
  outliers final: 5
  residues processed: 90
  average time/residue: 0.0452
  time to fit residues: 5.6200
Evaluate side-chains
  94 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  528 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0770
   chunk 25 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 29 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0770
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.3696

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.165143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.138811 restraints weight = 4723.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.143290 restraints weight = 2544.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.146615 restraints weight = 1645.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.148837 restraints weight = 1200.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.150287 restraints weight = 956.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.4064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3819  Z= 0.127
  Angle     :  0.612   8.852   5204  Z= 0.305
  Chirality :  0.039   0.162    611
  Planarity :  0.004   0.054    633
  Dihedral  :  4.070  16.175    520
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.14 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.41), residues: 478
  helix:  1.37 (0.28), residues: 373
  sheet:  None (None), residues: 0
  loop : -1.03 (0.65), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 384 
 TYR   0.019   0.001   TYR A 132 
 PHE   0.017   0.002   PHE A 442 
 TRP   0.018   0.001   TRP A 469 
 HIS   0.004   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 3819)
  covalent geometry    : angle       0.61226 /  0.30 ( 5204)
  hydrogen bonds       : bond        0.03303 /  2.17 (  279)
  hydrogen bonds       : angle       4.25775 /  2.83 (  825)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   36 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7514 (tp)
REVERT: A  100 TRP cc_start: 0.5796 (t60) cc_final: 0.5255 (t60)
REVERT: A  174 PHE cc_start: 0.5207 (OUTLIER) cc_final: 0.5004 (t80)
REVERT: A  342 MET cc_start: 0.8661 (mmm) cc_final: 0.8266 (mmt)
REVERT: A  361 SER cc_start: 0.8879 (m) cc_final: 0.8612 (t)
  outliers start: 9
  outliers final: 5
  residues processed: 97
  average time/residue: 0.0365
  time to fit residues: 4.9537
Evaluate side-chains
  99 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  397 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0670
   chunk 19 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.185537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.160007 restraints weight = 4633.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.164409 restraints weight = 2470.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.167240 restraints weight = 1574.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.169362 restraints weight = 1155.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.170902 restraints weight = 923.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3819  Z= 0.145
  Angle     :  0.628   8.345   5204  Z= 0.312
  Chirality :  0.040   0.163    611
  Planarity :  0.004   0.054    633
  Dihedral  :  4.079  16.276    520
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.65 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.40), residues: 478
  helix:  1.33 (0.28), residues: 373
  sheet:  None (None), residues: 0
  loop : -1.10 (0.66), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 136 
 TYR   0.013   0.001   TYR A 132 
 PHE   0.015   0.001   PHE A 137 
 TRP   0.019   0.001   TRP A 469 
 HIS   0.004   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.14 ( 3819)
  covalent geometry    : angle       0.62836 /  0.31 ( 5204)
  hydrogen bonds       : bond        0.03405 /  2.24 (  279)
  hydrogen bonds       : angle       4.28091 /  2.85 (  825)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A   36 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7493 (tp)
REVERT: A  100 TRP cc_start: 0.5819 (t60) cc_final: 0.5241 (t60)
REVERT: A  361 SER cc_start: 0.8841 (m) cc_final: 0.8534 (t)
REVERT: A  430 ILE cc_start: 0.7521 (mm) cc_final: 0.7282 (mm)
  outliers start: 11
  outliers final: 8
  residues processed: 97
  average time/residue: 0.0445
  time to fit residues: 6.0310
Evaluate side-chains
  101 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  561 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 10 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 25 optimal weight:    0.3980
   chunk 7 optimal weight:    0.1980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.185703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.160323 restraints weight = 4679.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.164715 restraints weight = 2516.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.167766 restraints weight = 1614.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.169700 restraints weight = 1170.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.171165 restraints weight = 935.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.4269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3819  Z= 0.143
  Angle     :  0.642   8.186   5204  Z= 0.315
  Chirality :  0.040   0.168    611
  Planarity :  0.004   0.054    633
  Dihedral  :  4.113  17.201    520
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.91 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.40), residues: 478
  helix:  1.31 (0.28), residues: 373
  sheet:  None (None), residues: 0
  loop : -1.14 (0.65), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 384 
 TYR   0.014   0.001   TYR A 132 
 PHE   0.017   0.002   PHE A  24 
 TRP   0.019   0.001   TRP A 469 
 HIS   0.003   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.14 ( 3819)
  covalent geometry    : angle       0.64152 /  0.31 ( 5204)
  hydrogen bonds       : bond        0.03341 /  2.20 (  279)
  hydrogen bonds       : angle       4.26377 /  2.83 (  825)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  956 Ramachandran restraints generated.
    478 Oldfield, 0 Emsley, 478 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   36 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7546 (tp)
REVERT: A  100 TRP cc_start: 0.5896 (t60) cc_final: 0.5398 (t60)
REVERT: A  361 SER cc_start: 0.8899 (m) cc_final: 0.8575 (t)
REVERT: A  523 TYR cc_start: 0.6848 (OUTLIER) cc_final: 0.4548 (m-80)
  outliers start: 9
  outliers final: 7
  residues processed: 94
  average time/residue: 0.0457
  time to fit residues: 5.7669
Evaluate side-chains
  98 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  238 HIS
Chi-restraints excluded: chain A residue  286 THR
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  379 MET
Chi-restraints excluded: chain A residue  397 MET
Chi-restraints excluded: chain A residue  523 TYR
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  561 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0870
   chunk 5 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.6358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.162776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.137231 restraints weight = 4694.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.141498 restraints weight = 2614.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.144526 restraints weight = 1721.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.146571 restraints weight = 1274.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.147972 restraints weight = 1029.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.4360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3819  Z= 0.149
  Angle     :  0.652   7.815   5204  Z= 0.318
  Chirality :  0.041   0.166    611
  Planarity :  0.004   0.053    633
  Dihedral  :  4.131  18.400    520
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 20.65 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.40), residues: 478
  helix:  1.32 (0.28), residues: 373
  sheet:  None (None), residues: 0
  loop : -1.15 (0.64), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 136 
 TYR   0.013   0.001   TYR A 132 
 PHE   0.014   0.002   PHE A 137 
 TRP   0.020   0.001   TRP A 469 
 HIS   0.004   0.001   HIS A 533 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.15 ( 3819)
  covalent geometry    : angle       0.65175 /  0.32 ( 5204)
  hydrogen bonds       : bond        0.03371 /  2.20 (  279)
  hydrogen bonds       : angle       4.28874 /  2.84 (  825)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 737.89 seconds
wall clock time: 13 minutes 26.09 seconds (806.09 seconds total)